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Congenital anomalies of gastrointestinal tract

Congenital anomalies of gastrointestinal tract (GIT) can be sometimes detected by the prenatal screening (ultrasound – polyhydramnios, direct visualisation of affected GIT; biochemistry – elevated alpha-fetoprotein in gastroschisis and omphalocele). Postnatal investigations include proper clinical examination (distended abdomen, vomiting with/without bilious aspirates) and imaging techniques (ultrasound, native or contrast radiography). The lower (distal) the obstruction in the GIT (atresia, stenosis), the later the malformation will be diagnosed (ileus).

Congenital GIT anomalies require surgery (urgent or delayed), followed by post-operative supervision in the intensive care unit (ventilation and circulation support, total parenteral nutrition).

Basic division:

  • cleft malformations of oral cavity
  • esophageal atresia
  • small intestine anomalies
  • large intestine anomalies
  • abdominal wall defects
  • congenital diaphragmatic hernia (CDH)

Cleft defects

Cleft defects of oral cavity (cleft lip – cheiloschisis, cleft palate – palatoschisis) can be complete or incomplete, unilateral or bilateral. The plastic surgery is performed early (within the first week of life, due to high concentrations of hyaluronic acid in the neonatal tissue, thus reducing post-operative scarring and speeding up tissue regeneration) or at later stage (around 3 months of age, decreased risk of surgical complications – infection, bleeding, anesthesia).

Complex, multidisciplinary approach is required and the care should be centralized (plastic surgeon, neonatologist/pediatrician, stomatologist, logopedist).

Esophageal atresia

Esophageal atresia with tracheoesophageal fistula requires urgent surgical intervention. There are several forms of the disorder, based on Vogt or Gross classification. The most common form is proximal blind esophageal part, the distal esophageal part is connected with trachea via fistula (Vogt 3B, 90% of cases). Other types include H-type (esophagus is not disconnected, communicates with trachea with fistula) or atresia without any tracheoesophageal fistula.

Clinical findings depend on the type of the atresia. For the most common type, there is apparent and significant salivating, the newborn has dyspnea, cyanosis and cough. Gastric tube cannot be put in and there is a risk of aspiration pneumonia, as well as chemical pneumonia (regurgitating gastric acid). The anomaly is diagnosed with contrast radiography. The newborn needs to be in elevated position, secretions must be suctioned from the proximal esophageal part to minimize the risk of aspiration.

There can be other associated malformations, that can form a syndrome (VACTERL – Vertebral anomalies, Anal atresia, Cardiovascular anomalies, TracheoEsophageal fistula-atresia, Renal anomalies, Limb defects).

H-type presents with cough, cyanosis, especially during feeding, the newborn can be without any problems between feeds; however, there is also risk of (recurrent) aspiration pneumonia.

Small intestine anomalies

Duodenal atresia

  • atresia, membrane, pancreas annulare (pancreas pushing on duodenum causes obstruction)
  • vomiting
  • X-ray = “”double bubble” (air in stomach and in the pre-stenotic part of duodenum)

Intestinal atresia

  • the more distal the anomaly is located, the later the symptoms can develop (delayed passage of meconium, significant gastric aspirates, vomiting, distended abdomen)
  • native or contrast radiography
  • duplications = tubular/cystic structures attached to the intestines, thus sharing common blood supply (duplications can present with obstruction, bleeding, inflammation)

Persistent ductus omphaloentericus

  • revealed after cutting umbilicus as another lumen with secretion
  • Meckel’s diverticulum = outpouching in the lower part of the small intestine (the most common congenital defect of the gastrointestinal tract)


  • suboptimal attachment of mesentery to the posterior wall of the abdominal cavity causes rotation (volvulus) of the small intestine (can be prenatal)
  • significant vomiting and distension of the abdomen
  • requires urgent surgery due to the high risk of intestinal gangrene => resection of necrotic parts causes short bowel syndrome (SBS)

Meconium ileus

  • terminal ileum obstruction due to thick meconium strongly adhering to the intestinal wall
  • can be a first symptom of cystic fibrosis
  • in case of intrauterine perforation, the meconium causes peritonitis with calcifications and fibrosis that can generate external pressure on intestines
  • distended abdomen with discoloration
  • native X-ray without typical “air-fluid levels”, irigography reveals microcolon

Large intestine anomalies

Meconium plug syndrome

  • neuromuscular intestinal immaturity, leading to transient retention and thickening of meconium (meconium plug) => transient obstruction of colon
  • vomiting, distended abdomen, absent meconium passage postnatally
  • native X-ray with distended intestinal loops
  • small left colon syndrome = presence of the meconium plug in the left colon
  • conservative management

Megacolon congenitum (Hirschsprung’s disease)

  • congenital absence of parasympathetic innervation of the distal colon
    → myenteric plexus – Auerbach (within the smooth muscle layers of the intestinal wall)
    → submucosal plexus – Meissner (within the submucosa of the gastrointestinal tract wall))
  • the affected portion is stenotic, in comparison to proximal dilated and hypertrophic portion (trying to overcome the functional obstruction)
  • delayed meconium passage, problematic stool passage at later stage, distended abdomen, vomiting
  • irigography (stenotic part with proximal dilatation), biopsy (anorectal mucosa)
  • surgical resection of abnormal section of colon (varying length)

Anorectal malformation

  • atresia/stenosis in the anorectal area are commonly associated with fistulas (to perineum, urinary bladder, vagina)
  • possible meconium/stool passage through the present fistula (facilitation) => delayed surgery
  • ultrasound, MRI of pelvis, X-ray (ileus)

Abdominal wall defects

Omphalocele (exomphalos)

  • failure of the intestines to return to the abdominal cavity during intrauterine development => permanent intestinal herniation (peritoneal sac) through the umbilicus can be diagnosed prenatally


  • congenital cleft of the abdominal wall, usually right of the umbilicus
  • herniation of small intestine (and other organs) = not covered by peritoneum => high risk of necrosis/gangrene
  • sterile, moist cover right after birth; antibiotics
  • urgent surgery => resection of necrotic parts => short bowel syndrome

Congenital diaphragmatic hernia

Herniation of abdominal organ to the thoracic cavity, due to the defect development of the diaphragm (usually on the left side). The herniation causes lung hypoplasia. CDH can be diagnosed prenatally, postnatal diagnosis usually arises when a newborn requires unplanned intensive resuscitation (respiratory failure) and responds poorly to ventilation – especially with resuscitation bag.

Most babies need to be intubated at the delivery suite and require very high inspiration pressures with 100% oxygen due to lung hypoplasia and concomitant pulmonary hypertension. Clinical findings include dyspnea, cyanosis, sunken abdomen with thorax in the inspiration position, heart sounds are deviated to the right in case of left-sided CDH. The diagnosis is confirmed by X-ray. Surgery is performed following the infant’s stabilization (ventilation, circulation).


① Burge DM. The management of bilious vomiting in the neonate. Early Hum Dev. 2016;102:41-45. doi:10.1016/j.earlhumdev.2016.09.002

② Leeuwen L, Fitzgerald DA. Congenital diaphragmatic hernia. J Paediatr Child Health. 2014;50(9):667-673. doi:10.1111/jpc.12508

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